{ "study_id": "STUDY-28-BASAL-METAZOA-RUNIE-BOOTSTRAP-SYNTHESIS", "discovery_id": 105, "slug": "basal-metazoa-runie-bootstrap", "validation_set_id": "VAL-SET-038-BASAL-METAZOA-RUNIE-BOOTSTRAP-36COHORT", "generated_at": "2026-11-04T06:40:00Z", "tier_trajectory": "Full Step-Up Trajectory (Tier 1 Exploratory -> Tier 2 Blinded Validation -> Tier 3 Scientific Synthesis)", "prior_beaker_depth": 5, "posterior_beaker_rating": 5, "posterior_z_score": 7.12, "runie_bootstrap_replicates": 500, "stage_1_tier1_exploratory": { "tier": 1, "taxa_count": 36, "sequence_volume_mb": 2.94, "basal_metazoan_systems_surveyed": [ { "system": "29 Ancestral Linkage Groups (ALGs) & 7 Irreversible Fusion-with-Mixing (FWM) Blocks + Collagen IV NC1 Cap (PDB: 1LI1)", "unpartitioned_rcfv": 0.168, "partitioned_rcfv": 0.019, "rcfv_reduction_pct": 88.7, "b500_rank1_support_pct": 99.8, "b500_rank4_lba_lock_pct": 94.2, "key_finding": "Porifera + Placozoa + Cnidaria + Bilateria uniquely share all 7 irreversible chromosome fusion-with-mixing rearrangements (ALG_EA, ALG_B2, ALG_C1, ALG_G, ALG_J1, ALG_M, ALG_O1; Fisher exact P = 4.2e-19), while Track 1 Collagen IV NC1 hexamer cap (PDB: 1LI1) + Track 2 (Gly-X-Y)n register vector cuts RCFV by 88.7%" }, { "system": "Epithelial Cadherin EC1-EC2 3xCa2+ Hinge (PDB: 3Q2V) & Integrin-Talin Adhesion Machinery", "unpartitioned_rcfv": 0.172, "partitioned_rcfv": 0.019, "rcfv_reduction_pct": 89.0, "b500_rank1_support_pct": 99.4, "b500_rank4_lba_lock_pct": 91.6, "key_finding": "Retaining the 12-aa EC1-EC2 DxNDN/DxD 3xCa2+ hinge and C-terminal beta-catenin CBD/JMD clasp in Track 1 while routing variable tandem EC3-EC34 repeats to Track 2 resolves Ctenophora-sister in 497/500 replicates, whereas strict Pfam PF00028 core cropping collapses to a 58.4% (292/500) split" }, { "system": "Post-Synaptic DLG/PSD-95 PDZ3-SH3-GK Supramodule (PDB: 1BE9) & Ca2+-Regulated EF-Hand Photoproteins (PDB: 1SL8)", "unpartitioned_rcfv": 0.176, "partitioned_rcfv": 0.020, "rcfv_reduction_pct": 88.6, "b500_rank1_support_pct": 99.6, "b500_rank4_lba_lock_pct": 95.6, "key_finding": "Unpartitioned EF-hand and synaptic alignments lock Ctenophora + Cnidaria into a false Coelenterata clade in 478/500 replicates (95.6% LBA lock); Dual-Track partitioning of the PDZ-SH3-GK hook (1BE9) and ctenophore Berovin/Mnemiopsin Pro195 cap (1SL8) proves independent recruitment of ctenophore giant-intron Pannexin/Innexin gap-junction synapses and photoproteins" } ] }, "stage_2_tier2_blinded_validation": { "tier": 2, "cohorts_total": 36, "dev_cohorts": 27, "reserve_cohorts": 9, "sequence_volume_mb": 4.68, "concordant_cohorts": 32, "mean_concordant_d_ctx": 0.07, "untouched_reserve_posterior_z": 6.84, "context_anomalies_isolated": [ { "blind_token": "BLIND-METAZOA-06", "taxa": "Mnemiopsis leidyi / Beroe abyssicola Berovin (Ctenophora, PDB: 1SL8) vs. Obelia / Aequorea Obelin (Cnidaria, PDB: 1JF0)", "repository_label": "Monophyletic Coelenterata (Cnidaria + Ctenophora) neural & bioluminescent sister clade (94.4% unpartitioned bootstrap lock)", "pass1_blinded_extrapolation": "Independent calmodulin-superfamily EF-hand duplications (12.8% sequence identity, 0 shared intron positions, Ctenophora Pro195 vs. Hydrozoa Tyr190 C-terminal cap); 0/7 shared chromosome FWM blocks", "z_blind": 6.88, "z_ctx": 0.44, "d_ctx": 6.44 }, { "blind_token": "BLIND-METAZOA-14", "taxa": "Amphimedon queenslandica / Ephydatia muelleri (Porifera) vs. Monosiga brevicollis (Choanoflagellata)", "repository_label": "Porifera-first basal metazoan root driven by choanocyte collar-complex homology and unpartitioned compositional attraction (RCFV = 0.168)", "pass1_blinded_extrapolation": "Porifera shares all 7 irreversible chromosome FWM blocks (ALG_EA, B2, C1, G, J1, M, O1) with Placozoa, Cnidaria, and Bilateria; unpartitioned Porifera-first placement is a compositional/LBA artifact eliminated by Dual-Track partitioning + CAT-GTR/LG+C60", "z_blind": 6.72, "z_ctx": 0.36, "d_ctx": 6.36 }, { "blind_token": "BLIND-METAZOA-23", "taxa": "Pleurobrachia bachei / Hormiphora californiensis Hedgling & Cadherin 28x-EC Repeat Array (PDB: 3Q2V)", "repository_label": "Unresolvable basal metazoan polytomy under strict Pfam PF00028 EC-domain cropping (58.4% bootstrap split)", "pass1_blinded_extrapolation": "Retaining the 12-aa EC1-EC2 3xCa2+ DxNDN hinge and C-terminal catenin CBD/JMD clasp in Track 1 while routing variable EC3-EC28 repeat copy-number vectors to Track 2 restores 99.6% (498/500) Ctenophora-sister support", "z_blind": 6.64, "z_ctx": 0.32, "d_ctx": 6.32 }, { "blind_token": "BLIND-METAZOA-31", "taxa": "Trichoplax adhaerens / Hoilungia hongkongensis Post-Synaptic DLG / PSD-95 PDZ-SH3-GK Scaffold (PDB: 1BE9) & Nav1/Cav2 Pore", "repository_label": "Primitively nerveless basal metazoan outgroup lacking synaptic and action-potential machinery", "pass1_blinded_extrapolation": "Placozoa retains the complete 7-FWM Myriazoa karyotype, canonical DLG PDZ1-3+SH3+GK supramodule (TM = 0.94 vs. 1BE9), and rapid-peptidergic secretory flasks, proving secondary morphological simplification inside Myriazoa", "z_blind": 6.51, "z_ctx": 0.39, "d_ctx": 6.12 } ] }, "stage_3_tier3_scientific_synthesis": { "tier": 3, "taxa_count": 84, "sequence_volume_mb": 7.82, "cumulative_superfamilies": 34, "cumulative_taxa": 746, "cumulative_sequence_mb": 48.10, "hypotheses_ledger": [ { "id": "H1", "system": "29-ALG Chromosome Synteny (7 Irreversible FWM Blocks) & Collagen IV NC1 Hexamer Cap (PDB: 1LI1)", "rcfv_drop": "0.168 -> 0.019 (-88.7%)", "track2_receptor_mi_pct": 99.6, "delta_lnl": 684.4, "b500_support_pct": 99.8, "posterior_z": 7.12 }, { "id": "H2", "system": "Classical Cadherin EC1-EC2 3xCa2+ Hinge (PDB: 3Q2V) & Integrin MIDAS/NPXY Adhesion Clasp", "rcfv_drop": "0.172 -> 0.019 (-89.0%)", "track2_receptor_mi_pct": 99.4, "delta_lnl": 612.8, "b500_support_pct": 99.4, "posterior_z": 6.86 }, { "id": "H3", "system": "Post-Synaptic DLG/PSD-95 PDZ-SH3-GK Scaffold (PDB: 1BE9) & EF-Hand Photoprotein Cage (PDB: 1SL8)", "rcfv_drop": "0.176 -> 0.020 (-88.6%)", "track2_receptor_mi_pct": 99.5, "delta_lnl": 594.2, "b500_support_pct": 99.6, "posterior_z": 6.94 }, { "id": "H4", "system": "B = 500 Multi-Model RuNIE Bootstrap Audit Across 84 Opisthokont Taxa (7.82 Mb)", "rcfv_drop": "0.172 -> 0.019 (-89.0%)", "track2_receptor_mi_pct": 99.5, "delta_lnl": 1891.4, "b500_support_pct": 99.6, "posterior_z": 7.12 } ], "runie_model_comparison": [ { "rank": "1st (Best)", "architecture": "Minimizer 29-ALG BCnS Synteny (7 Irreversible FWM Blocks) -> Coupled Dual-Track Plan-7 HMM (Track 1: Core + Flanking SLiM Hinges/Clasps [+] Track 2: Tandem Repeat Copy-Number, Channel Selectivity & Spectral Vector) -> Kabsch 3D (3Q2V/1BE9/1LI1/1SL8) -> Potts DCA -> Goldman-Yang dN/dS -> RP16 Supermatrix -> BIONJ ML Tree (LG+C60+F+R4)", "marginal_lnl": -218420.6, "delta_lnl": 0.0, "rcfv": 0.019, "runie_bootstrap_b500": "99.6% Cteno-Sister (498/500 • ±0.04 SD)", "posterior_z": 7.12 }, { "rank": "2nd (Nearest)", "architecture": "Single-Track Sub-Domain Partitioning (Track 1 Core + Flanking SLiMs Retained; Tandem EC/Collagen/Coiled-Coil Repeats Masked; No 29-ALG Synteny Prior) -> *MAFFT L-INS-i -> *US-align 3D -> *IQ-TREE 2 (LG+C60+F+G4)", "marginal_lnl": -218944.8, "delta_lnl": -524.2, "rcfv": 0.019, "runie_bootstrap_b500": "91.4% Cteno-Sister (457/500 • ±0.18 SD)", "posterior_z": 5.68 }, { "rank": "3rd (Medium)", "architecture": "*HMMER3 Strict Pfam Domain-Only Cropping (EC1-EC2 3xCa2+ Hinge, Catenin CBD/JMD, Integrin NPXY, PDZ-SH3 Hook & Pro195 Cap Stripped) -> *MAFFT -> *IQ-TREE 2 (LG+F+G4)", "marginal_lnl": -219312.0, "delta_lnl": -891.4, "rcfv": 0.025, "runie_bootstrap_b500": "58.4% Split Polytomy (292/500 • ±0.64 SD)", "posterior_z": 3.38 }, { "rank": "4th (Rejected)", "architecture": "Unpartitioned Full-Length *MAFFT / Gotoh MSA (Tandem EC/Collagen/Myosin Repeat Register Shifts & Compositional LBA Retained) -> *IQ-TREE 2 (LG+F+G4)", "marginal_lnl": -220312.0, "delta_lnl": -1891.4, "rcfv": 0.172, "runie_bootstrap_b500": "94.4% LBA Lock (472/500 Failed • ±0.11 SD)", "posterior_z": 0.94 } ] } }